A sequencing batch reactor (SBR) with alternating anaerobic/oxic (An/O) operation was employed to investigate nitrogen and phosphorus removal performance and corresponding phosphate recovery effect of an enhanced biological phosphorus removal (EBPR) system when extracting side stream ratios of 0, 1/4, 1/3, 1/2 anaerobic phosphorus supernatant. The operation involved three runs within 310 days. Removal efficiencies of COD and NH4+-N were found to be relatively stable over the entire experimental period and effluent could meet standard A of the national discharge standard of pollutants for municipal wastewater treatment plants. Total nitrogen removal improved due to enhancement of denitrification capability during the anaerobic phase, and the standard-reaching rate increased from 88.2% to 98.6%. Although phosphate releasing capability gradually decreased, phosphorus removal performances of the former two runs were stable and efficient. The removal rate was>90% and the corresponding standard-reaching rate was>75%. Nevertheless, phosphorus removal performance began to fluctuate with a side stream ratio of 1/2 during the third run. The lowest phosphorus removal rate was 54.2%, contributing to a 60% non-standard-reaching rate in this run. This suggests that long-term extraction of 1/2 side stream supernatant is not favorable for maintaining stable effluent of the main process. It was also found that long-term phosphate recovery through side stream extraction allowed reduction of sludge mass and had little impact on sludge settling performance. As a result, it is feasible to extract an appropriate side stream ratio of anaerobic supernatant to recover phosphate, combined with efficient removal of both nitrogen and phosphorus in the main process.